plot_state_comparison: State deuterium uptake comparison

In HaDeX2: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

State deuterium uptake comparison

Description

Comparison plot of deuterium uptake values in time point for biological states.

Usage

plot_state_comparison(
  uptake_dat,
  skip_amino = 0,
  theoretical = FALSE,
  fractional = FALSE,
  line_size = 1.5,
  all_times = FALSE,
  time_t = NULL,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

uptake_dat	data produced by calculate_state_uptake function
skip_amino	integer, indicator how many amino acids from the N-terminus should be omitted
theoretical	logical, indicator if values are calculated using theoretical controls
fractional	logical, indicator if values are shown in fractional form
line_size	line size for the plot
all_times	logical, indicator is all all time should be plotted next to each other
time_t	chosen time point
interactive	logical, whether plot should have an interactive layer created with with ggiraph, which would add tooltips to the plot in an interactive display (HTML/Markdown documents or shiny app)

Details

The function plot_state_comparison generates a comparison plot, presenting deuterium uptake values of peptides from selected protein in selected biological states at one time point of measurement at once. On X-axis there is a position in a sequence, with length of a segment of each peptide representing its length. On Y-axis there is deuterium uptake in selected form. Error bars represents the combined and propagated uncertainty.

Value

a ggplot object

See Also

read_hdx calculate_state_uptake

Examples

uptake_dat <- calculate_state_uptake(alpha_dat)
plot_state_comparison(uptake_dat)

plot_state_comparison(uptake_dat, all_times = TRUE)
plot_state_comparison(uptake_dat, fractional = TRUE, all_times = TRUE)

HaDeX2 documentation built on Feb. 9, 2026, 5:07 p.m.